Both versions contain footage that's missing in the other one, but the Theatrical Version lacks way more footage. Furthermore several scenes have been removed and reinsert afterwards in the TV Version, some of them are edited differently. But these differences aren't mentioned in this comparison because it would break the mold. David Lychn's version is the Theatrical Version btw. He wasn't involved in the TV Version and ordered that his name in the opening credits was going to be replaced by Alan Smithee (common alias for directors who don't want their name in a version). The main difference in the two versions is the fact that the TV Version has been split up to smaller episodes. As a result of that, the movie doesn't look like a motion picture anymore but like a big TV production. Unfortunately, this doesn't make the movie better at all. On the contrary, it makes it worse. Really awful is the aspect ratio because the TV Version comes along in Pan&Scan. A lot of atmosphere gets lost because of this.

Example:
Theatrical Version | TV Version

That's one of the more harmless scenes. There are some scenes where it's way more conspicuous.

Therefore the TV Version is only attractive for people who want anything complete or for hardcore fans of Dune.

Compared are the longer TV Version and the Theatrical Version.A comparison about the missing footage in the TV Version can be found here.

Missing footage Theatrical Version: 3073 min = 51:12 minThe difference in running time is due to roundings of the removed footage, short black images (ad) in the TV Version and probably some scenes I missed (sorry if that is really an issue).

00:17 MinAfter the collimation "A David Alan Smythe" (it's just David Lynch in the Theatrical Version), a woman comes up with some deets about spice and the planet Arakis (Dune).
97 sec

01:40 MinThe following prolog is completely different in either of the versions.

Theatrical Version:
Classified report about the conspiracy to sabotage the spice extraction on the screen. Four planets (Arrakis, Caladan, Giedi Prime and Kaitain) are under suspicion and a third-degree navigator ought to be send to Kaitain to get information about the conspiracy from the emperor. "The spice needs to flow"

39 sec

10:10 MinThe emperor turns around and drops his coat. Then a high-angle shot of the space harbor.
9 sec

11:32 MinDuring the sentence "...Report when we finish", the TV Version contains a 2 sec-shot of Helen Mohiam (Bene Gesserit).
(2 sec) no differenceTV Version on the left, Theatrical Version on the right

13:03 MinShot of the navigator's mouth (?) in the Theatrical Version. The TV Version contains a shot of the emperor in the first 2 sec instead.
(4 sec) no differenceTV Version on the left, Theatrical Version on the right

13:03 MinThe TV Version contains a shot of Helen Mohiam at the telepathy during the question "How was your yourney?".
(3 sec) no differenceTV Version on the left, Theatrical Version on the right

13:51 MinAfter the missing dialog in the Theatrical Version:
Alternate angle when the navigator explains it was aware of the hostility of the two houses and adds the emperor was hiding sth. The Theatrical Version shows a third person perspective from the emperor most of the time, the TV Version shows the emperor's front instead.
10 Sek.secTV Version on the left, Theatrical Version on the right

14:22 MinShot of the navigator during the dialog - shot of the emperor in the Theatrical Version.
(2 sec) no differenceTV Version on the left, Theatrical Version on the right

14:28 MinHelen Mohiam is transmitting thoughts again - shot of the emperor and an extended shot of the navigator in the Theatrical Version.
(3 sec) no differenceTV Version on the left, Theatrical Version on the right

15:47 MinShot from the emperor's POV at the end of the dialog in the Theatrical Version, shot from the other side in the TV Version.
(5 sec) no differenceTV Version on the left, Theatrical Version on the right

20:05 MinShot of the ring coming closer to the camera in the Theatrical Version. The TV Version contains a couple of shots of the planet instead.
(5 sec) no differenceTV Version on top, Theatrical Version below

38:40 MinHere's one more dialog scene, but therefore another scene is missing. The Theatrical Version contains a shot of a Freme asking Paul to tell about about his homeland, followed by a shot of Helen Mohiam's face. She puts her hand off Paul's forehead and says "Do you now..."
6 sec

43:39 MinShot of two of the baron's assistants plus shot of blood flowing in a jar plus a slightly extended tracking shot to the baron's face.
9 sec

During the following conversation with the baron, the voices are deeper and anything is a little slower (that just sucks!).

45:41 MinShot of one the baron's assistants, then a removed shot of the room. Close-up of one the two guys who just came in, he has a worm or sth. in a jar. He pushes the cover and squashes the worm, then he drinks sth. through a straw. The baron laughs. While the baron's assistant is kissing ass, a man is being brought in by two security guards. He puts some flowers in a couple of bins. While doing, the baron says "I will have Arakis back for myself!". The TV Version shows a shot of two guys during that sentence instead.
46 sec

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47:29 MinThe baron's bloodbath is longer. He goes to the man, who was brought in by the security guards, and pulls the plug out of his heart. Blood is leaking and the baron pushes him against the wall. Then a couple of shots of the present people. Finally blood splatters on the wall and the man slides down the wall, leant against the baron.
46 sec

49:17 MinAfter Paul looked at his mother, a shot of her is missing. She thinks at the night with her husband. While being in bed, they hug and she tells him she was going to miss Caladan.
21 sec